Background. Limited data exist regarding left atrial appendage (LAA) thrombi and spontaneous echocardiographic contrast (SEC) in patients with atrial flutter (AFL). Objectives. We sought to evaluate the LAA thrombi prevalzence in AFL ablation patients compared to atrial fibrillation (AFib) ablation patients. Methods and Results. 321 consecutive patients referred for either AFib (n = 229) or AFL ablation (n = 92) were included with a thrombus detected by transesophageal echocardiography (TEE) in 3.22% (12/321). The percentage of thrombi was similar between AFL and AFib ablation patients (5.4% [n = 5/92] vs. 3.1% [n = 7/229]; p = 0.3). In the overall population, LAA thrombi patients had a higher CHA²DS²-VASc score (3 ± 2 vs. 2 ± 1.5; p = 0.048) and a higher presence of valvular prothesis (25% vs. 4.9%; p=0.003), with relevant left atrial remodeling such as demonstrated by a higher left atrium (LA) volume (57 ± 19 vs. 46 ± 17 ml/m²; p = 0.04) and a lower LAA velocity (0.41 ± 0.3 vs. 0.55 ± 0.2; p=0.04). In patients with right AFL, patients with LAA thrombi had a higher CHA²DS²-VASc score (4.4 ± 1 vs. 2.5 ± 1.5; p = 0.008), had more hypertension (100% vs. 53%; p = 0.04) and more diabetes mellitus (60% vs. 18.4%; p = 0.03), and a more severe LAA echo contrast (80% vs. 5.7%; p <0.0001). Conclusions. The risk of LAA thrombi is better related to the presence of valvular prosthesis, CHA²DS²-VASc score and LA remodelling than the atrial arrhythmia itself.